Warren A. Kibbe
| Warren A. Kibbe|
(Alternative names for this author)
|Co-authors||Andrew I. Su, Benjamin M. Good, Bradley I. Arshinoff, Douglas G. Howe, Eric M. Just, Garret Suen, John D. Osborne, Rex L. Chisholm, Roy D. Welch, Simon Lin, Simon M. Lin, Sohel M. Merchant|
|Authorship||Publications (3), datasets (0), tools (0)|
|Citations||Total (1), average (0.333333333333), median (0), max (1), min (0)|
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Warren A. Kibbe is an author.
PublicationsOnly those publications related to wikis are shown here.
|Title||Keyword(s)||Published in||Language||DateThis property is a special property in this wiki.||Abstract||R||C|
|Mining the Gene Wiki for functional genomic knowledge||BMC genomics||English||2011||Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborative platform for assembling text-based gene annotations. The Gene Wiki is comprised of more than 10,000 review articles, each describing one human gene. The goal of this study is to define and assess a computational strategy for translating the text of Gene Wiki articles into ontology-based gene annotations. We specifically explore the generation of structured annotations using the Gene Ontology and the Human Disease Ontology. RESULTS: Our system produced 2,983 candidate gene annotations using the Disease Ontology and 11,022 candidate annotations using the Gene Ontology from the text of the Gene Wiki. Based on manual evaluations and comparisons to reference annotation sets, we estimate a precision of 90-93% for the Disease Ontology annotations and 48-64% for the Gene Ontology annotations. We further demonstrate that this data set can systematically improve the results from gene set enrichment analyses. The Gene Wiki is a rapidly growing corpus of text focused on human gene function. Here, we demonstrate that the Gene Wiki can be a powerful resource for generating ontology-based gene annotations. These annotations can be used immediately to improve workflows for building curated gene annotation databases and knowledge-based statistical analyses.||0||0|
|Other riffs on cooperation are already showing how well a wiki could work||English||2007||0||1|
|Xanthusbase: adapting Wikipedia principles to a model organism database||Nucleic Acids Research||English||2007||xanthusBase (http://www.xanthusbase.org) is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanistic basis of prokaryotic multicellularity, a topic that has garnered considerable attention due to the significance of biofilms in both basic and applied microbiology research. To facilitate its utility, the design of xanthusBase incorporates open-source software, leveraging the cumulative experience made available through the Generic Model Organism Database (GMOD) project, MediaWiki (http://www.mediawiki.org), and dictyBase (http://www.dictybase.org), to create a MOD that is both highly useful and easily navigable. In addition, we have incorporated a unique Wikipedia-style curation model which exploits the internet's inherent interactivity, thus enabling M.xanthus and other myxobacterial researchers to contribute directly toward the ongoing genome annotation.||0||0|